MOLDRAW can also prepare Gaussian98 input file for a two-layers ONIOM
calculation (three-layers are still non supported). ONIOM method has been
introduced by Maseras and Morokuma (F. Maseras and K. Morokuma, J.
Comp. Chem.16, 1170 (1995)) to treat complex molecular systems by
dividing the system in two regions, one treated with a high level of theory
(accurate but expensive) while the whole system (the second region) is computed
with a lower level of theory (rough but cheap). An example of the ONIOM
application from the author's work can
be downloaded here.
As an example, the silasesquioxyde
H4O7Si4 molecule is considered. The SiOH
terminal silanol is a functionality where hydrogen bond interaction may
occur, so that high level of theory should be used for this fragment.
Open the (Edit--->Assign and edit ONIOM atoms) menu
to select the atoms belonging to the high level region. Atoms belonging to
the high region will appear in white colour. Any atom can be set again to
the low level region by selecting Low
level on the ONIOM dialog and clicking the offending
atom.
The structure is ready to be exported to Gaussian (Export label in the toolbar).
A dialog already containing a two-level ONIOM setup pops up. Default
values are B3LYP/6-31+G(d,p) and MNDO for the high and low level
calculations, respectively.
The resulting Gaussian input file is shown below. MOLDRAW automatically
assigns the proper molecular mechanics symbol for the various atoms, so that
both UFF and
DREIDING molecular mechanics calculations can be performed. In the present
case, the oxygen atoms linked to two silicon atoms are correctly assigned the
O-O_3_z symbol.
%chk=moldraw.chk %mem= 32MB #P TEST
OPT ONIOM(B3LYP/6-31+G(d,p):MNDO) 5D SCF=DIRECT
GEOM=(PrintInputOrient,NODISTANCE,NOANGLE,NODIHEDRAL)
Input made
by MOLDRAW 03/09/2006
0
1 H
0 0.9285768006
3.2493208960 1.5298112333
H O
0 0.1615527168
2.9445453293 1.0331238021
H SI 0
0.1064071201 1.4072237980 0.5089069682
H O-O_3_z 0
0.1708459137 0.2657282227 1.7271221830
L H 3 SI
0 0.0464501128
-1.3365143320 1.2594038596
L H
0 0.0956971661 -2.2650433577
2.3863098745 L O-O_3_z 0
1.3451094021 0.9944346347 -0.5334147574
L H 3 SI
0 1.3064735413 -0.5545883327
-1.1662267882
L H
0 2.4149791976 -0.8257789130
-2.0784655011
L O
0 -1.3089581944 1.1306467771
-0.3154791442 L H
3 SI
0 -1.5275724194 -0.4119935442
-0.9263263156 L H
0 -2.7951196997 -0.5679635460
-1.6350476830 L O
0 -1.3761325088 -1.4439254766
0.3838726990 L O
0 -0.1931938384 -0.7098355533
-1.8933645557 L O
0 1.2799887491
-1.5831456685 0.1545631251 L
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